Module 477

General Properties
Below we list the number of gene sets from which the module was composed was originally composed, and the number of genes and experiments that it contains. Clicking on the number of genes will display a detailed list of all the genes in the module. Clicking on the number of experiments will display a detailed list of all the experiments in the module.
Num gene sets:	4
Num genes:	53 (see 713 additional genes for this module)
Num experiments:	332 (108 induced, 224 repressed)
Parent module:	None
Children modules:	None

Gene sets
Below we list the gene sets from which the module was originally composed. Clicking on a gene set will display all the genes associated with that gene set. Also listed are all the other modules in which the gene set participates.
Iyer99 5
Rosenwald01 47
tumor suppressor
Cuadras02 49

Enriched clinical annotations
For each of the clinical annotations, we tested whether it was enriched in the set of arrays in which the module is significantly induced (or repressed). Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of induced (or repressed) module's arrays in which they appear. We also show the fraction of the module's induced (or repressed) arrays with the given annotation ('Hits (%)' column). For completeness, we also list the total number of relevant induced arrays in the module ('Module hits in category' column), total number of arrays in the compendium in which the corresponding annotation is present ('Arrays in annotation' column), and the total number of relevant arrays in the compendium ('Arrays' column). Note that the 'relevant' arrays may be different for each annotation, since it includes only arrays in which the annotation was relevant (i.e., present or not present) and excludes arrays where the value of the annotation was not known. Rows that correspond to annotations that were enriched in the induced arrays of the module have a red background, while rows corresponding to annotations enriched in the repressed arrays have a green background. For each annotation, we also list the other modules in which it was enriched.
Clinical annotation	Category	P-value	Hits	Hits(%)	Module hits in category	Arrays in annotation	Arrays
CNS tissue, cancer or cell line (General compendium)	General compendium	6.8e-20	61	27.3	223	164	1946
CNS tumor (General compendium)	General compendium	2.8e-19	56	25.1	223	144	1946
CNS cancer or cell line (General compendium)	General compendium	1.6e-17	56	25.1	223	155	1946
Cancer and cell line (General compendium)	General compendium	4.6e-14	206	92.3	223	1429	1946
Lung carcinoid (Lung cancer)	Lung cancer	1.1e-08	15	29.4	51	20	276
Cancer (General compendium)	General compendium	2.0e-08	165	73.9	223	1110	1946
Cell line (Breast cancer)	Breast cancer	2.2e-08	10	100	10	30	152
Liver tissue (General compendium)	General compendium	2.6e-07	28	26.1	107	187	1946
Liver tissue, cancer or cell line (General compendium)	General compendium	8.2e-07	28	26.1	107	197	1946
Epithelial cell line (Breast cancer)	Breast cancer	9.6e-06	7	70	10	18	152
Cancer and cell line (Liver cancer)	Liver cancer	1.4e-05	21	100	21	126	207
Lung cancer (General compendium)	General compendium	1.8e-05	49	21.9	223	244	1946
Lung cancer or cell line (General compendium)	General compendium	2.9e-05	51	22.8	223	262	1946
Breast cancer cell line (Breast cancer)	Breast cancer	0.0001	6	60	10	17	152
Hepatitis infected liver (General compendium)	General compendium	0.0001	20	18.6	107	156	1946
Lung tissue, cancer or cell line (General compendium)	General compendium	0.0002	54	24.2	223	304	1946
Large cell lung cancer (Lung cancer)	Lung cancer	0.0003	3	23.0	13	4	276

Enriched GO annotations
For each GO annotation, we tested whether it was enriched in the set of genes of the module. Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of the module's genes in which they appear. We also show the fraction of the module's genes with the given GO annotation that are included in this module ('Hits (%)' column). For completeness, we also list the total number of genes in the module ('Module genes' column), total number of genes in the compendium in which the corresponding annotation is present ('Genes in annotation' column), and the total number of genes in the compendium ('Genes' column).

Visual display

Below is a visual display of the module. Shown are those arrays in which the module's genes significantly change, and the direction of change (induction/repression) in each array is indicated (middle, labeled 'Module changes'; red/green row). The arrays that correspond to the significant clinical attributes are also shown (top; brown rows). The gene sets that compose the module are also shown (left) along with an indication of the membership of the module genes in these gene sets.

You can also view the images within GeneXPress by loading the module gxp file file.

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